Visualizing cells at the nanoscale

Trends in Biochemical Sciences

Volumn 34, Issue 2, 2009, Pages 60-70

  Leis, Andrew ^a   Rockel, Beate ^a   Andrees, Lars ^a   Baumeister, Wolfgang ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CELL STRUCTURE; CORRELATION ANALYSIS; CYTOARCHITECTURE; CYTOLOGY; ELECTRON MICROSCOPY; EUKARYOTIC CELL; MACROMOLECULE; MOLECULAR BIOLOGY; NANOANALYSIS; PRIORITY JOURNAL; PROKARYOTIC CELL; REVIEW; TOMOGRAPHY; ULTRAMICROTOMY; VITRIFICATION; X RAY;

ANIMALS; CELLS; CRYOELECTRON MICROSCOPY; ELECTRON MICROSCOPE TOMOGRAPHY; HUMANS; IMAGING, THREE-DIMENSIONAL;

EUKARYOTA; PROKARYOTA;

EID: 59649086100     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2008.10.011     Document Type: Review

References (89)

1. Nickell S., et al. A visual approach to proteomics. Nat. Rev. Mol. Cell Biol. 7 (2006) 225-230
2. Robinson C.V., et al. The molecular sociology of the cell. Nature 450 (2007) 973-982
3. Heuser J. Whatever happened to the 'microtrabecular concept'?. Biol. Cell 94 (2003) 561-596
4. Kistler J., and Kellenberger E. Collapse phenomena in freeze-drying. J. Ultrastruct. Res. 59 (1977) 70-75
5. Anderson T.F. Some fundamental limitations to the preservation of 3-dimensional specimens for the electron microscope. Trans. N. Y. Acad. Sci. 16 (1954) 242-249
6. Parsons D.F. Structure of wet specimens in electron-microscopy. Science 186 (1974) 407-414
7. Matricardi V.R., et al. Electron-diffraction of wet proteins - catalase. Science 177 (1972) 268-270
8. Taylor K.A., and Glaeser R.M. Electron-diffraction of frozen, hydrated protein crystals. Science 186 (1974) 1036-1037
9. Zhang X., et al. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 1867-1872
10. Ellis R.J. Macromolecular crowding: obvious but underappreciated. Trends Biochem. Sci. 26 (2001) 597-604
11. Dubochet J., and McDowall A.W. Vitrification of pure water for electron microscopy. J. Microsc. 124 (1981) RP3-RP4
12. Jiang W., and Ludtke S.J. Electron cryomicroscopy of single particles at subnanometer resolution. Curr. Opin. Struct. Biol. 15 (2005) 571-577
13. Henderson R. Realizing the potential of electron cryo-microscopy. Q. Rev. Biophys. 37 (2004) 3-13
14. Ludtke S.J., et al. De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure 16 (2008) 441-448
15. Nickell S., et al. Structural analysis of the 26S proteasome by cryoelectron tomography. Biochem. Biophys. Res. Commun. 353 (2007) 115-120
16. Nitsch M., et al. Group II chaperonin in an open conformation examined by electron tomography. Nat. Struct. Biol. 5 (1998) 855-857
17. Heide H.G. On the irradiation of organic-samples in the vicinity of ice. Ultramicroscopy 7 (1982) 299-300
18. Kürner J., et al. Cryo-electron tomography reveals the cytoskeletal structure of Spiroplasma melliferum. Science 307 (2005) 436-438
19. Medalia O., et al. Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science 298 (2002) 1209-1213
20. Nicastro D., et al. The molecular architecture of axonemes revealed by cryoelectron tomography. Science 313 (2006) 944-948
21. Gruska M., et al. Electron tomography of vitreous sections from cultured mammalian cells. J. Struct. Biol. 161 (2008) 384-392
22. Le Gros M.A., et al. X-ray tomography of whole cells. Curr. Opin. Struct. Biol. 15 (2005) 593-600
23. Schneider G. Cryo X-ray microscopy with high spatial resolution in amplitude and phase contrast. Ultramicroscopy 75 (1998) 85-104
24. Larabell C.A., and Le Gros M.A. X-ray tomography generates 3-D reconstructions of the yeast, Saccharomyces cerevisiae, at 60-nm resolution. Mol. Biol. Cell 15 (2004) 957-962
25. Chao W., et al. Soft X-ray microscopy at a spatial resolution better than 15 nm. Nature 435 (2005) 1210-1213
26. Baumeister W. Mapping molecular landscapes inside cells. Biol. Chem. 385 (2004) 865-872
27. Hegerl R., and Hoppe W. Influence of electron noise on three-dimensional image reconstruction. Z. Naturforsch. A 31 (1976) 1717-1721
28. Dierksen K., et al. 3-Dimensional structure of lipid vesicles embedded in vitreous ice and investigated by automated electron tomography. Biophys. J. 68 (1995) 1416-1422
29. Baumeister W. From proteomic inventory to architecture. FEBS Lett. 579 (2005) 933-937
30. Crowther R.A., et al. The reconstruction of a three-dimensional structure from its projections and its applications to electron microscopy. Proc. R. Soc. Lond. A Math. Phys. Sci. 317 (1970) 319-340
31. Cardone G., et al. A resolution criterion for electron tomography based on cross-validation. J. Struct. Biol. 151 (2005) 117-129
32. Radon J. Über die Bestimmung von Funktionen durch ihre Integralwerte längs gewisser Mannigfaltigkeiten. Berichte über die Verhandlungen der Königlich Sächsischen Gesellschaft der Wissenschaften zu Leipzig. Math. Phys. Klasse 69 (1917) 262-277
33. Nickell S., et al. Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography. J. Struct. Biol. 141 (2003) 34-42
34. Mastronarde D.N. Dual-axis tomography: An approach with alignment methods that preserve resolution. J. Struct. Biol. 120 (1997) 343-352
35. Lučić V., et al. Structural studies by electron tomography: from cells to molecules. Annu. Rev. Biophys. Biomol. Struct. 74 (2005) 833-865
36. Wolter H. Spiegelsysteme streifenden Einfalls als abbildende Optiken für Röntgenstrahlen. Ann. Phys.-Berlin 10 (1952) 94-114
37. Grimm R., et al. Determination of the inelastic mean free-path in ice by examination of tilted vesicles and automated most probable loss imaging. Ultramicroscopy 63 (1996) 169-179
38. Grimm R., et al. Zero-loss energy filtering under low-dose conditions using a post-column energy filter. J. Microsc. 183 (1996) 60-68
39. Afzelius B.A., and Maunsbach A.B. Biological ultrastructure research; the first 50 years. Tissue Cell 36 (2004) 83-94
40. Moor H. Theory and practice of high pressure freezing. In: Steinbrecht R.A., and Zierold K. (Eds). Cryotechniques in Biological Electron Microscopy (1987), Springer-Verlag 175-191
41. Courties C., et al. Smallest eukaryotic organism. Nature 370 (1994) 255
42. Matsuzaki M., et al. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428 (2004) 653-657
43. Marko M., et al. Focused-ion-beam thinning of frozen-hydrated biological specimens for cryoelectron microscopy. Nat. Methods 4 (2007) 215-217
44. Studer D., et al. A new approach for cryofixation by high-pressure freezing. J. Microsc. 203 (2001) 285-294
45. Shimoni E., and Müller M. On optimizing high-pressure freezing: from heat transfer theory to a new microbiopsy device. J. Microsc. 192 (1998) 236-247
46. Gilkey J.C., and Staehelin A. Advances in ultrarapid freezing for the preservation of cellular ultrastructure. J. Electron Microsc. Tech. 3 (1986) 177-210
47. Ding B., et al. Effect of high-pressure freezing on plant microfilament bundles. J. Microsc. 165 (1991) 367-376
48. Leforestier A., et al. Comparison of slam-freezing and high pressure freezing effects on the DNA cholesteric liquid crystalline structure. J. Microsc. 184 (1996) 4-13
49. Dubochet J., et al. Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 21 (1988) 129-228
50. Zuber B., et al. The mammalian central nervous synaptic cleft contains a high density of periodically organized complexes. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 19192-19197
51. Hsieh C.E., et al. Towards high-resolution three-dimensional imaging of native mammalian tissue: Electron tomography of frozen-hydrated rat liver sections. J. Struct. Biol. 153 (2006) 1-13
52. Heller C. Finding a universal low-viscosity polymer for DNA separation. Electrophoresis 19 (1998) 1691-1698
53. Sartori A., et al. Correlation microscopy: Bridging the gap between light- and cryo-electron microscopy. Microsc. Microanal. 11 (2005) 16-17
54. Leis A., et al. Cryo-electron tomography and fluorescence microscopy of unicellular algae in vitreous cryosections. Microsc. Microanal. 11 (2005) 330CD
55. Schwartz C.L., et al. Cryo-fluorescence microscopy facilitates correlations between light and cryo-electron microscopy and reduces the rate of photobleaching. J. Microsc. 227 (2007) 98-109
56. Sartori A., et al. Correlative microscopy: bridging the gap between fluorescence light microscopy and cryo-electron tomography. J. Struct. Biol. 160 (2007) 135-145
57. Lučić V., et al. Cryo-electron tomography of cells: Connecting structure and function. Histochem. Cell Biol. 130 (2008) 185-196
58. Al-Amoudi A., et al. An oscillating cryo-knife reduces cutting-induced deformation of vitreous ultrathin sections. J. Microsc. 212 (2003) 26-33
59. Lefman J., et al. Three-dimensional electron microscopic imaging of membrane invaginations in Escherichia coli overproducing the chemotaxis receptor Tsr. J. Bacteriol. 186 (2004) 5052-5061
60. Studer D., and Gnaegi H. Minimal compression of ultrathin sections with use of an oscillating diamond knife. J. Microsc. 197 (2000) 94-100
61. Heymann J.A.W., et al. Site-specific 3D imaging of cells and tissues with a dual beam microscope. J. Struct. Biol. 155 (2006) 63-73
62. Knott G., et al. Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling. J. Neurosci. 28 (2008) 2959-2964
63. Denk W., and Horstmann H. Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol. 2 (2004) e329
64. Tokuyasu K.T. Immunochemistry on ultrathin frozen-sections. Histochem. J. 12 (1980) 381-403
65. Kireev I., et al. In vivo immunogold labeling confirms large-scale chromatin folding motifs. Nat. Methods 5 (2008) 311-313
66. Mercogliano C.P., and DeRosier D.J. Gold nanocluster formation using metallothionein: Mass spectrometry and electron microscopy. J. Mol. Biol. 355 (2005) 211-223
67. Grabenbauer M., et al. Correlative microscopy and electron tomography of GFP through photooxidation. Nat. Methods 2 (2005) 857-862
68. Frangakis A.S., et al. Identification of macromolecular complexes in cryoelectron tomograms of phantom cells. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 14153-14158
69. Beck M., et al. Nuclear pore complex structure and dynamics revealed by cryoelectron tomography. Science 306 (2004) 1387-1390
70. Beck M., et al. Snapshots of nuclear pore complexes in action captured by cryo-electron tomography. Nature 449 (2007) 611-615
71. Sali A., et al. From words to literature in structural proteomics. Nature 422 (2003) 216-225
72. McGill G. Molecular movies... coming to a lecture near you. Cell 133 (2008) 1127-1132
73. Kemp M. Seeing the smaller picture. Nature 453 (2008) 596
74. Adams, M.W.W. (1999) The influence of environment and metabolic capacity on the size of a microorganism. In Size Limits of Very Small Microorganisms (Knoll, A., ed.), pp.74-80, Space Studies Board/National Research Council
75. Schulz H.N., et al. Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science 284 (1999) 493-495
76. La Scola B., et al. A giant virus in amoebae. Science 299 (2003) 2033
77. Rendulic S., et al. A predator unmasked: Life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science 303 (2004) 689-692
78. Partensky F., et al. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol. Mol. Biol. Rev. 63 (1999) 106-127
79. Huber H., et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417 (2002) 63-67
80. Hell S.W., et al. Concepts for nanoscale resolution in fluorescence microscopy. Curr. Opin. Neurobiol. 14 (2004) 599-609
81. Donnert G., et al. Macromolecular-scale resolution in biological fluorescence microscopy. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 11440-11445
82. Ludtke S.J., et al. Seeing GroEL at 6 Å resolution by single particle electron cryomicroscopy. Structure 12 (2004) 1129-1136
83. Gonen T., et al. Lipid-protein interactions in double-layered two-dimensional AQPO crystals. Nature 438 (2005) 633-638
84. Jelsch C., et al. Accurate protein crystallography at ultra-high resolution: Valence electron distribution in crambin. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 3171-3176
85. Cordwell S.J., et al. Proteome analysis of Spiroplasma melliferum (A56) and protein characterisation across species boundaries. Electrophoresis 18 (1997) 1335-1346
86. Ortiz J.O., et al. Mapping 70S ribosomes in intact cells by cryoelectron tomography and pattern recognition. J. Struct. Biol. 156 (2006) 334-341
87. Goddard T.D., et al. Visualizing density maps with UCSF Chimera. J. Struct. Biol. 157 (2007) 281-287
88. Herman G.T., and Rowland S. Resolution in ART - Experimental investigation of resolving power of an algebraic picture reconstruction technique. J. Theor. Biol. 33 (1971) 213-223
89. Gilbert P. Iterative methods for 3-dimensional reconstruction of an object from projections. J. Theor. Biol. 36 (1972) 105-117